Comparing Whole-Exome Sequencing to Gene Panels

Genetic testing is now available for more than 2,000 rare and common diseases. Many of these clinical tests are based on single-gene analysis or microarrays and cost up to $10,000 per test. Working in the Center for Applied Genomics, headed by Dr. Steven Scherer and part of the Hospital for Sick Children in Toronto, Canada, Dr. Christian Marshall is assessing the utility (and possible clinical validity in the future) of Ion Proton™ whole-exome sequencing as a possible future replacement for microarray and single-gene testing.

The Center provides project support to hundreds of investigators involved in local, nationwide, and international research initiatives, including experimentation, statistical analysis, and comprehensive bioinformatics support. The Center’s bioinformatics efforts include large-scale genome comparisons, algorithm and tools development, and database curation, annotation, and hosting. Dr. Marshall is using the Ion Proton™ sequencer in its efforts to assess cost-effectiveness in the Center’s operations, in particular its accuracy comparing concordance to its existing gene panels, and the overall yield of whole-exome sequencing. The Center’s researchers investigate both rare diseases and complex disorders.

While less than 1% of the genome, the exome contains more than 85%of disease-causing mutations. Until the cost of whole-genome sequencing is reduced, research using whole-exome sequencing provides a cost-effective alternative for identifying SNVs (single nucleotide variants), copy number variations, small indels, and rare unknown mutations that may be associated with complex conditions. However, whole-exome sequencing also vastly increases the data with which a laboratory has to work.

To test the ability of whole-exome (and possibly whole-genome) sequencing to replace traditional methods, Marshall and his colleagues looked at samples from 25 previously diagnosed subjects with a range of diseases, from rare disorders like focal segmental glomerulosclerosis (FSGS), cone-rod dystrophy, ocular albinism, and Stargardt disease, to more complex disorders like epilepsy, hypertrophic cardiomyopathy, and autism spectrum disorder.

Marshall’s team found that the Ion Proton System sequenced exomes quickly and inexpensively, and found very high concordance of calls between gene panels and Ion Proton sequencing. In the case of an archived sample of focal segmental glomerulosclerosis (FSGS, a disorder affecting at least 5,400 people in North America per year) Proton sequencing revealed a mutation in the PLC1 gene that was not on the standard FSGS gene panel.

Looking at an archived sample of the very rare disorder Adam’s-Oliver Syndrome (only 100 have been cited in the medical literature), Ion Torrent sequencing did not find mutations in four targeted genes, but did uncover a mutation in a fifth. The team performed trio sequencing of the affected proband and parental samples, and found new mutations in the gene ACVR1, which is associated with a disorder similar to Adam’s-Oliver.

Using 2,000 samples from subjects previously diagnosed with autism (and about 75 parent-proband trio samples), the team compared microarray and whole-exome sequencing data, including over one million SNP microarrays and copy number variations. Autism has complex causes; the team is looking now at about 125 genes known to be associated with autism. So far, the team has discovered that not all 125 genes need to be mutated in autism. In fact, many cases could be caused by just one or two variants.

The team found that constructing the library, preparing the template, Ion Torrent sequencing, and analyzing data could be performed in days. Dr. Marshall’s research projects underscored the utility and potential value of using whole-genome sequencing in diagnostic labs of the future, as the cost of whole-exome sequencing quickly becomes lower than standard genetic tests.

You can view Dr. Christian Marshall’s entire recorded talk for the AAAS’s Science Technology Webinar Series discussing Exome Sequencing in Today’s Lab here.